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#541 hetero [128] is not seen as ligand

open
Bob Hanson
5
2012-11-21
2012-11-21
Angel Herraez
No

2gvd.pdb has a ligand named [128]
which is not selected as "ligand" by Jmol 13.0.8

It is selected as "nucleic" due to ? being a nucleotide analog --though rather different

Discussion

  • Bob Hanson
    Bob Hanson
    2012-11-21

    correct. The definition of "ligand" was changed in 12.2. From the documentation:

    (originally "hetero and not solvent"; changed to "!(protein,nucleic,water,UREA)"

    I think you just have to work with that. Nothing I can think of would be the perfect "ligand" definition.

     
  • Angel Herraez
    Angel Herraez
    2012-11-21

    Yes, I was aware of the ligand redefintion --and I am happy with it, I think it's better.

    The issue is why this ligand should be recognized as nucleic. It is quite different from a nucleotide. I guess it has the proper atom IDs to fit into Jmol algorithm?

    I assume there is no solution for this. The problem was, using standard defualt rendering of a pdb, the ligand is invisible.

    Perhaps single-residue "proteins" and "nucleics" could be selected somehow and applied ball and stick instead of cartoon... Something similar to C-only proteins and P-only nucleics getting a specific treatment.

     
  • Bob Hanson
    Bob Hanson
    2012-11-21

    I like the idea of single-residue groups rendering in ball and stick.